Kerry said that the difficulty for US planes accessing Incirlik may have been a result of planes flown in support of the coup using the air base to refuel.
It is unclear whether aircraft from the base were hijacked by coup plotters during the overnight events. Turkey is a member of the North Atlantic Treaty Organisation alliance.
The base has been a springboard for aerial attacks against ISIS in Syria and Iraq.
An A-10 squadron has been based at Incirlik since October 2015, after the Turkish government allowed USA strike aircraft to use the base.
Reacting to the closure of the base, the United States said that they were working to "minimize and effects" on the war against the terrorist group ISIS. Some 10 other soldiers and one police officer based in Incirlik were also detained.
Even though President Barack Obama said he backed the elected government during the coup attempt, insinuations that the U.S. supported anti-Erdoğan forces were potent enough that Secretary of State John Kerry issued a strongly worded denial late Saturday.
Whatever happens, veteran Turkey watchers said they were flabbergasted by the coup attempt, given that Mr. Erdogan appeared to have a near-monopoly on power. The 1980 "September 12 Coup" helped end a period of anarchy and terror, but not before thousands of people were arrested and dozens were executed and tortured.
Ankara mayor Melih Gocek stated the officer who shot down the Russian fighter jet was arrested as one of the coup organizers.
General Bekir Ercan Van was detained, the official said. It could also complicate the Pentagon's ability to resupply and aid the US special forces inside Syria. "We will continue to take the necessary steps to ensure the safety and security of our service members, our civilians, their families and our facilities".
The reasons for the closure were unclear, but there was speculation it could be to put pressure on the United States over Fetullah Gulen, a cleric who has lived in self-imposed exile in the USA for years and whose followers the Turkish government has said were behind the coup.
But if the government fails to maintain the upper hand it claimed on saturday to have, the US could be bound by laws that prohibit partnering with countries where military forces overthrow a democratically elected government.